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CHECK report for birte on tokay2

This page was generated on 2019-10-16 12:32:25 -0400 (Wed, 16 Oct 2019).

Package 175/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
birte 1.20.0
Holger Froehlich
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/birte
Branch: RELEASE_3_9
Last Commit: a84a8e5
Last Changed Date: 2019-05-02 11:53:53 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  ERROR  skipped 
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  ERROR  skipped  skipped 

Summary

Package: birte
Version: 1.20.0
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:birte.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings birte_1.20.0.tar.gz
StartedAt: 2019-10-16 02:18:05 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 02:20:40 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 155.2 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: birte.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:birte.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings birte_1.20.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/birte.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'birte/DESCRIPTION' ... OK
* this is package 'birte' version '1.20.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'birte' can be installed ... WARNING
Found the following significant warnings:
  BayesNetwork.cpp:383:14: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  getStates.cpp:349:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
  getStates.cpp:366:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
  getStates.cpp:384:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/birte.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
birte.aux: no visible global function definition for 'is'
birteRun: no visible global function definition for 'is'
birteStart: no visible global function definition for 'is'
Undefined global functions or variables:
  is
Consider adding
  importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/birte/libs/i386/birte.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/birte/libs/x64/birte.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
simulateData  7.42   0.12    7.55
birtePredict  6.64   0.13    6.77
birteRun      6.17   0.15    6.33
birteFitRidge 6.00   0.12    6.12
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
birteFitRidge 5.53   0.13    5.75
birtePredict  5.26   0.07    5.34
birteRun      5.08   0.05    5.13
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/birte.Rcheck/00check.log'
for details.

Installation output

birte.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/birte_1.20.0.tar.gz && rm -rf birte.buildbin-libdir && mkdir birte.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=birte.buildbin-libdir birte_1.20.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL birte_1.20.0.zip && rm birte_1.20.0.tar.gz birte_1.20.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  306k  100  306k    0     0  4669k      0 --:--:-- --:--:-- --:--:-- 5199k

install for i386

* installing *source* package 'birte' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c BayesNetwork.cpp -o BayesNetwork.o
In file included from BayesNetwork.cpp:26:0:
BayesNetwork.h:203:3: warning: "/*" within comment [-Wcomment]
   /**
 ^
BayesNetwork.cpp: In constructor 'BayesNetwork::BayesNetwork(int, int, int, int, int, int**, double***, double***, double***, double***, int, int, int, int, int, double*, double*, double*, double*, std::list*, std::list*, std::list*, std::list*, std::list*, std::list*, double, double, double, double, double, double, double, double, double, double*, double*, double*, double*, double*, double*, int, int, std::list*, std::list*, std::list*, double*, double*, double*, double**, int**, int**, int**, int**, double**, double**, double**)':
BayesNetwork.cpp:96:8: warning: unused variable 'j' [-Wunused-variable]
  int i,j,c,r;
        ^
BayesNetwork.cpp:96:12: warning: unused variable 'r' [-Wunused-variable]
  int i,j,c,r;
            ^
BayesNetwork.cpp: In destructor 'virtual BayesNetwork::~BayesNetwork()':
BayesNetwork.cpp:221:8: warning: unused variable 'i' [-Wunused-variable]
  int c,i,j;
        ^
BayesNetwork.cpp:221:10: warning: unused variable 'j' [-Wunused-variable]
  int c,i,j;
          ^
BayesNetwork.cpp: In member function 'virtual int BayesNetwork::expandDesignMatrix(int, int, int, std::list*, double**, int)':
BayesNetwork.cpp:357:6: warning: unused variable 'found' [-Wunused-variable]
  int found, omega_index = 0, i, j;
      ^
BayesNetwork.cpp:357:30: warning: unused variable 'i' [-Wunused-variable]
  int found, omega_index = 0, i, j;
                              ^
BayesNetwork.cpp: In member function 'virtual int BayesNetwork::shrinkDesignMatrix(int, int, int)':
BayesNetwork.cpp:383:14: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
   if(p.first == switchid & p.second == mir){
              ^
BayesNetwork.cpp:380:11: warning: unused variable 'k' [-Wunused-variable]
  int j=1, k, del=-1;  // j startet bei 1, weil die 1. Spalte der Intercept ist
           ^
BayesNetwork.cpp: In member function 'virtual void BayesNetwork::updateEvidence2(int, int, int, arma::colvec&)':
BayesNetwork.cpp:599:11: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    if(add != R[c].n_cols){
           ^
BayesNetwork.cpp: In member function 'virtual double BayesNetwork::swap_states(int**, int, int, std::set*, std::list*, std::set**, double)':
BayesNetwork.cpp:669:14: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(swapid1 >= swap_idx[condition].size()) {
              ^
BayesNetwork.cpp:665:6: warning: unused variable 'pos_swaps' [-Wunused-variable]
  int pos_swaps = 0, condition, condition1, condition2, counter;
      ^
BayesNetwork.cpp: In member function 'virtual void BayesNetwork::MCMC(long int, long int, int, double*)':
BayesNetwork.cpp:842:6: warning: unused variable 'mir' [-Wunused-variable]
  int mir, tf;
      ^
BayesNetwork.cpp:842:11: warning: unused variable 'tf' [-Wunused-variable]
  int mir, tf;
           ^
BayesNetwork.cpp:847:7: warning: unused variable 'eff_samples' [-Wunused-variable]
  long eff_samples = niter / thin + 1;
       ^
BayesNetwork.cpp:909:23: warning: unused variable 'u' [-Wunused-variable]
  double delta_loglik, u, delta_prior, eps_new, eps_old, delta_eps, best_loglik=-INFINITY; 
                       ^
BayesNetwork.cpp:909:26: warning: unused variable 'delta_prior' [-Wunused-variable]
  double delta_loglik, u, delta_prior, eps_new, eps_old, delta_eps, best_loglik=-INFINITY; 
                          ^
BayesNetwork.cpp:909:39: warning: unused variable 'eps_new' [-Wunused-variable]
  double delta_loglik, u, delta_prior, eps_new, eps_old, delta_eps, best_loglik=-INFINITY; 
                                       ^
BayesNetwork.cpp:909:48: warning: unused variable 'eps_old' [-Wunused-variable]
  double delta_loglik, u, delta_prior, eps_new, eps_old, delta_eps, best_loglik=-INFINITY; 
                                                ^
BayesNetwork.cpp:909:57: warning: unused variable 'delta_eps' [-Wunused-variable]
  double delta_loglik, u, delta_prior, eps_new, eps_old, delta_eps, best_loglik=-INFINITY; 
                                                         ^
BayesNetwork.cpp:910:102: warning: unused variable 'make_move_eps' [-Wunused-variable]
  int nall_possible_ops, n_Tpos_swaps_total=0, n_Spos_swaps_total=0, n_Qpos_swaps_total=0, make_move, make_move_eps=0, cond=0;
                                                                                                      ^
BayesNetwork.cpp:910:119: warning: unused variable 'cond' [-Wunused-variable]
  int nall_possible_ops, n_Tpos_swaps_total=0, n_Spos_swaps_total=0, n_Qpos_swaps_total=0, make_move, make_move_eps=0, cond=0;
                                                                                                                       ^
BayesNetwork.cpp: In member function 'virtual double BayesNetwork::likelihood()':
BayesNetwork.cpp:1074:12: warning: unused variable 'j' [-Wunused-variable]
  int c, i, j, r;
            ^
BayesNetwork.cpp:1075:9: warning: unused variable 'bn' [-Wunused-variable]
  double bn; 
         ^
BayesNetwork.cpp:1078:9: warning: unused variable 'z' [-Wunused-variable]
  double z;
         ^
BayesNetwork.cpp: In member function 'virtual void BayesNetwork::MCMC(long int, long int, int, double*)':
BayesNetwork.cpp:1026:26: warning: 'delta_loglik' may be used uninitialized in this function [-Wmaybe-uninitialized]
   log_lik += delta_loglik;
                          ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c getStates.cpp -o getStates.o
In file included from getStates.cpp:24:0:
BayesNetwork.h:203:3: warning: "/*" within comment [-Wcomment]
   /**
 ^
getStates.cpp: In function 'SEXPREC* getStates(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
getStates.cpp:349:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
    if(S2O == NULL | SparentsOfO == NULL)
           ^
getStates.cpp:366:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
    if(T2O == NULL | TparentsOfO == NULL)
           ^
getStates.cpp:384:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
    if(Q2O == NULL | QparentsOfO == NULL)
           ^
Loading required package: Rcpp
Loading required package: Rcpp
Loading required package: Rcpp
Loading required package: Rcpp
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o birte.dll tmp.def BayesNetwork.o getStates.o -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/i386 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/birte.buildbin-libdir/00LOCK-birte/00new/birte/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'birte'
    finding HTML links ... done
    EColiNetwork                            html  
    EColiOxygen                             html  
    TFexpr                                  html  
    birteFitRidge                           html  
    finding level-2 HTML links ... done

    birtePredict                            html  
    birteRun                                html  
    estimateNetwork                         html  
    getPotentialSwaps                       html  
    humanNetwork                            html  
    limmaAnalysis                           html  
    plotConvergence                         html  
    proposeInteractions                     html  
    simplify                                html  
    simulateData                            html  
    suggestThreshold                        html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'birte' ...
** libs
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c BayesNetwork.cpp -o BayesNetwork.o
In file included from BayesNetwork.cpp:26:0:
BayesNetwork.h:203:3: warning: "/*" within comment [-Wcomment]
   /**
 ^
BayesNetwork.cpp: In constructor 'BayesNetwork::BayesNetwork(int, int, int, int, int, int**, double***, double***, double***, double***, int, int, int, int, int, double*, double*, double*, double*, std::list*, std::list*, std::list*, std::list*, std::list*, std::list*, double, double, double, double, double, double, double, double, double, double*, double*, double*, double*, double*, double*, int, int, std::list*, std::list*, std::list*, double*, double*, double*, double**, int**, int**, int**, int**, double**, double**, double**)':
BayesNetwork.cpp:96:8: warning: unused variable 'j' [-Wunused-variable]
  int i,j,c,r;
        ^
BayesNetwork.cpp:96:12: warning: unused variable 'r' [-Wunused-variable]
  int i,j,c,r;
            ^
BayesNetwork.cpp: In destructor 'virtual BayesNetwork::~BayesNetwork()':
BayesNetwork.cpp:221:8: warning: unused variable 'i' [-Wunused-variable]
  int c,i,j;
        ^
BayesNetwork.cpp:221:10: warning: unused variable 'j' [-Wunused-variable]
  int c,i,j;
          ^
BayesNetwork.cpp: In member function 'virtual int BayesNetwork::expandDesignMatrix(int, int, int, std::list*, double**, int)':
BayesNetwork.cpp:357:6: warning: unused variable 'found' [-Wunused-variable]
  int found, omega_index = 0, i, j;
      ^
BayesNetwork.cpp:357:30: warning: unused variable 'i' [-Wunused-variable]
  int found, omega_index = 0, i, j;
                              ^
BayesNetwork.cpp: In member function 'virtual int BayesNetwork::shrinkDesignMatrix(int, int, int)':
BayesNetwork.cpp:383:14: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
   if(p.first == switchid & p.second == mir){
              ^
BayesNetwork.cpp:380:11: warning: unused variable 'k' [-Wunused-variable]
  int j=1, k, del=-1;  // j startet bei 1, weil die 1. Spalte der Intercept ist
           ^
BayesNetwork.cpp: In member function 'virtual void BayesNetwork::updateEvidence2(int, int, int, arma::colvec&)':
BayesNetwork.cpp:599:11: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    if(add != R[c].n_cols){
           ^
BayesNetwork.cpp: In member function 'virtual double BayesNetwork::swap_states(int**, int, int, std::set*, std::list*, std::set**, double)':
BayesNetwork.cpp:669:14: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(swapid1 >= swap_idx[condition].size()) {
              ^
BayesNetwork.cpp:665:6: warning: unused variable 'pos_swaps' [-Wunused-variable]
  int pos_swaps = 0, condition, condition1, condition2, counter;
      ^
BayesNetwork.cpp: In member function 'virtual void BayesNetwork::MCMC(long int, long int, int, double*)':
BayesNetwork.cpp:842:6: warning: unused variable 'mir' [-Wunused-variable]
  int mir, tf;
      ^
BayesNetwork.cpp:842:11: warning: unused variable 'tf' [-Wunused-variable]
  int mir, tf;
           ^
BayesNetwork.cpp:847:7: warning: unused variable 'eff_samples' [-Wunused-variable]
  long eff_samples = niter / thin + 1;
       ^
BayesNetwork.cpp:909:23: warning: unused variable 'u' [-Wunused-variable]
  double delta_loglik, u, delta_prior, eps_new, eps_old, delta_eps, best_loglik=-INFINITY; 
                       ^
BayesNetwork.cpp:909:26: warning: unused variable 'delta_prior' [-Wunused-variable]
  double delta_loglik, u, delta_prior, eps_new, eps_old, delta_eps, best_loglik=-INFINITY; 
                          ^
BayesNetwork.cpp:909:39: warning: unused variable 'eps_new' [-Wunused-variable]
  double delta_loglik, u, delta_prior, eps_new, eps_old, delta_eps, best_loglik=-INFINITY; 
                                       ^
BayesNetwork.cpp:909:48: warning: unused variable 'eps_old' [-Wunused-variable]
  double delta_loglik, u, delta_prior, eps_new, eps_old, delta_eps, best_loglik=-INFINITY; 
                                                ^
BayesNetwork.cpp:909:57: warning: unused variable 'delta_eps' [-Wunused-variable]
  double delta_loglik, u, delta_prior, eps_new, eps_old, delta_eps, best_loglik=-INFINITY; 
                                                         ^
BayesNetwork.cpp:910:102: warning: unused variable 'make_move_eps' [-Wunused-variable]
  int nall_possible_ops, n_Tpos_swaps_total=0, n_Spos_swaps_total=0, n_Qpos_swaps_total=0, make_move, make_move_eps=0, cond=0;
                                                                                                      ^
BayesNetwork.cpp:910:119: warning: unused variable 'cond' [-Wunused-variable]
  int nall_possible_ops, n_Tpos_swaps_total=0, n_Spos_swaps_total=0, n_Qpos_swaps_total=0, make_move, make_move_eps=0, cond=0;
                                                                                                                       ^
BayesNetwork.cpp: In member function 'virtual double BayesNetwork::likelihood()':
BayesNetwork.cpp:1074:12: warning: unused variable 'j' [-Wunused-variable]
  int c, i, j, r;
            ^
BayesNetwork.cpp:1075:9: warning: unused variable 'bn' [-Wunused-variable]
  double bn; 
         ^
BayesNetwork.cpp:1078:9: warning: unused variable 'z' [-Wunused-variable]
  double z;
         ^
BayesNetwork.cpp: In member function 'virtual void BayesNetwork::MCMC(long int, long int, int, double*)':
BayesNetwork.cpp:1026:26: warning: 'delta_loglik' may be used uninitialized in this function [-Wmaybe-uninitialized]
   log_lik += delta_loglik;
                          ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c getStates.cpp -o getStates.o
In file included from getStates.cpp:24:0:
BayesNetwork.h:203:3: warning: "/*" within comment [-Wcomment]
   /**
 ^
getStates.cpp: In function 'SEXPREC* getStates(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
getStates.cpp:349:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
    if(S2O == NULL | SparentsOfO == NULL)
           ^
getStates.cpp:366:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
    if(T2O == NULL | TparentsOfO == NULL)
           ^
getStates.cpp:384:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
    if(Q2O == NULL | QparentsOfO == NULL)
           ^
Loading required package: Rcpp
Loading required package: Rcpp
Loading required package: Rcpp
Loading required package: Rcpp
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o birte.dll tmp.def BayesNetwork.o getStates.o -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/x64 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/birte.buildbin-libdir/birte/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'birte' as birte_1.20.0.zip
* DONE (birte)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'birte' successfully unpacked and MD5 sums checked

Tests output

Example timings

birte.Rcheck/examples_i386/birte-Ex.timings

nameusersystemelapsed
birteFitRidge6.000.126.12
birtePredict6.640.136.77
birteRun6.170.156.33
estimateNetwork000
getPotentialSwaps0.510.080.59
limmaAnalysis000
plotConvergence000
proposeInteractions0.410.050.45
simplify0.310.080.39
simulateData7.420.127.55
suggestThreshold0.550.000.55

birte.Rcheck/examples_x64/birte-Ex.timings

nameusersystemelapsed
birteFitRidge5.530.135.75
birtePredict5.260.075.34
birteRun5.080.055.13
estimateNetwork000
getPotentialSwaps0.590.080.67
limmaAnalysis000
plotConvergence000
proposeInteractions0.360.060.42
simplify0.250.090.34
simulateData4.270.104.36
suggestThreshold0.360.000.36